tbuckley/cabot-search huggingface dataset:
Abstract 3298: Two detection methods of clinical KRAS G12C mutation detection for companion diagnostics
Authors: Robert William Brown, Wei Liu, Qing Sun, Hui Ren, Jonathan Li, Larry Pastor, Daniel Kim, Michael Sha, Aiguo Zhang
Journal: Cancer Research (2023)

Abstract KRAS G12C is a common mutation in approximately 13% of lung adenocarcinoma, 3% of colorectal cancer and 2% of other solid tumors. The FDA approved sotorasib, a KRAS G12C inhibitor, for targeted treatment of patients with KRAS G12C-mutated locally or metastatic non-small cell lung cancer (NSCLC). It is essential to detect the KRAS G12C mutation with a companion diagnostic before the drug is administered. We have developed two KRAS G12C mutation detection assays for qPCR or Sanger sequencing. Both QClamp® assays use our proprietary xeno nucleic acid (XNA) technology which specifically enhances the amplification of the target mutant DNA sequence while blocking amplification of the wildtype sequence, thus significantly improving the sensitivity of the assays for qPCR (~1%) and Sanger sequencing (~15 to 20%) to 0.1% variant allele frequency. These simple and sensitive assays can be used for clinical research or validated in CLIA labs for KRAS G12C mutation detection for the purpose of companion diagnostic use. Although NGS methods are gaining traction in clinical settings, our methods are suitable for standard molecular diagnostics laboratory settings and do not add any additional steps to the qPCR or Sanger sequencing protocols. Our methods are especially valuable for labs that appreciate simple, economical, yet sensitive companion diagnostics assays for KRAS G12C mutation. QClamp® assays can be easily adapted to detect other single gene mutations with high sensitivity for companion diagnostics use or other mutation detection applications. Citation Format: Robert William Brown, Wei Liu, Qing Sun, Hui Ren, Jonathan Li, Larry Pastor, Daniel Kim, Michael Sha, Aiguo Zhang. Two detection methods of clinical KRAS G12C mutation detection for companion diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3298.
Abstract 2494: Heterogeneous tumor-driven immune landscapes between lung adenocarcinomas in ever and never-smokers
Authors: Xiaozheng Kang, Xin Wang, Liyan Ji, Bingfa Yan, Xuan Gao, Xuefeng Xia, Xingsheng Hu
Journal: Cancer Research (2023)

Abstract To depict the genomic and immune landscapes of lung adenocarcinomas (ADCs) in ever and never-smokers and guide the design of immunotherapy strategies, we applied multiple deconvolution methods that allow the identification of immune cell infiltration and immune pathway enrichment using a whole exome and transcriptome sequencing-based approach in 145 patient-matched lung ADC and non-malignant lung parenchymal tissue pairs from ever and never smokers in our in-house cohort. Results were subsequently validated by an external lung ADC cohort, including 108 never-smokers and 61 ever-smokers. Firstly, we showed that ever-smokers had an increased abundance of neutrophils and macrophage infiltration, an elevated antigen processing and presentation capacity, and activated T-cell-mediated immunity. Secondly, ever-smokers revealed elevated macrophages in acinar ADCs, decreased mast cells in lepidic ADCs, and increased neutrophils in papillary ADCs, suggesting the tumor-driven immune characteristic discrepancies among various pathologic subtypes of ADC. Thirdly, we identified mutational disparities in tumor mutation burdens, subclonal single nucleotide variants, and the predicted and expressed neoantigens between ever and never-smokers. The mutant gene KRAS preferably occurred in ever-smokers, further contributing to the infiltration of macrophages and expression of cytokines. The copy number variations of immune-related genes (NFIB, TNFAIP3) were identified as conferring to the dysregulated immune environment in ever-smokers. Moreover, a higher genomic instability index was observed in ever-smokers (p = 0.008). Fourthly, the neoantigen was significantly increased in ever-smoker lung ADCs without nodal disease. While DNA immunoediting preferably occurred in never-smokers. Notably, in lung ADC patients with nodal disease, ever-smokers exhibited slightly more homogenous mutations (p = 0.094), consistent with the evolutionary bottleneck during cancer progression. Finally, the lower immunoediting and higher microenvironment scores significantly determined the more prolonged progression-free survival in never-smokers (p &amp;lt; 0.050). Our multiscale genomic and immune profiling analyses thus offer valuable knowledge of tumor-driven immune disparity arising from smoking and provide a robust solution to the rational design of immune therapies. Citation Format: Xiaozheng Kang, Xin Wang, Liyan Ji, Bingfa Yan, Xuan Gao, Xuefeng Xia, Xingsheng Hu. Heterogeneous tumor-driven immune landscapes between lung adenocarcinomas in ever and never-smokers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2494.
Abstract 3982: Anti-Stanniocalcin 1 antibody as a potential therapeutic strategy for liver fibrosis and hepatocellular carcinoma
Authors: Alfred Long-Hin Suen, Kristy Kwan-Shuen Chan, Regina Cheuk-Lam Lo
Journal: Cancer Research (2023)

Abstract Introduction: Hepatocellular carcinoma (HCC) is the sixth most frequently diagnosed cancer and the third leading cause of cancer deaths. Liver fibrosis (LF) is a progressive disease and cirrhosis, the advanced stage of LF, is per se a risk factor for HCC. Moreover, LF persists after the development of HCC. Stanniocalcin 1 (STC1), as a serum biomarker of both HCC and LF as we previously reported, was found to be secreted from HCC cells and hepatic stellate cells (HSCs). STC1 promoted cell migration and invasion of HCC and activation of HSCs, suggesting that STC1 could be an actionable target of both diseases. As a secretory protein, STC1 could potentially be targeted by an antibody approach. Objectives: This study aims to investigate the therapeutic values of targeting secretory STC1 in HCC and LF models using antibody approach, including in the interplay between HSCs and HCC cells. Methods: Human anti-STC1 antibody was harvested and purified from a hybridoma cell line of a designed epitope. In vitro transwell migration and invasion assays were performed on human HCC cell lines. Co-culture assays were set up with HCC cells cultured in conditioned medium (CM) collected from LX2, a human HSC cell line. Expression of fibrogenic markers were measured by western blotting, qPCR and ELISA. Results: Enforcement of STC1, either by viral transfection of STC1-overexpressing vector or by the treatment of recombinant STC1 protein, increased the migration and invasion of HCC cells. The effects were abrogated by the co-treatment of anti-STC1 antibody. The enhanced migratory and invasive abilities of HCC cells induced by activated HSC CM were abolished by anti-STC1 antibody. In addition, anti-STC1 antibody suppressed the secretion of type I collagen (COL1) and the intracellular expression of fibrogenic markers alpha-smooth muscle actin (ɑSMA) and TIMP metallopeptidase inhibitor 1 (TIMP1) in TGFβ1-activated HSCs. Conclusion: Anti-STC1 antibody displays therapeutic effects on HCC in vitro. It is also shown to suppress the expression of fibrogenic markers in activated HSCs. Anti-STC1 antibody is a potential therapeutic strategy for both HCC and LF. Citation Format: Alfred Long-Hin Suen, Kristy Kwan-Shuen Chan, Regina Cheuk-Lam Lo. Anti-Stanniocalcin 1 antibody as a potential therapeutic strategy for liver fibrosis and hepatocellular carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3982.
Abstract 5848: Identification of mechanosensitive cancer associated fibroblasts in pancreatic cancer
Authors: Weikun Xiao, Chae-Young Eun, Weian Zhao, Reginald Hill
Journal: Cancer Research (2023)

Abstract The purpose of this study is to investigate whether a subpopulation of cancer associated fibroblasts (CAFs) are responsible for mechanosensation-mediated chemoresistance in pancreatic adenocarcinoma (PDAC). PDAC is one of the most lethal types of cancer with few effective treatments. The abundant stromal cells and the stiff desmoplastic microenvironment constitute more than 90% of the primary tumor bulk. However, there are few easily tunable models to recapitulate this stiff microenvironment. To address this issue, we have developed a Matrigel-based, orthogonally tunable 3-dimensional (3D) culture system to co-culture mouse derived PDAC organoids and host-matching cancer-associated fibroblasts (CAFs). Using this biomimetic model and a mechano-sensation-dependent reporter, we have identified a unique subpopulation of CAFs responsible for mechano-sensing the fibrotic matrix and facilitating CAF-mediated chemoresistance. Moreover, these mechanosensitive CAFs (mecCAFs) respond to increased stiffness through YAP-mediated pathways. Our results also demonstrate how ECM stiffness affects chemoresistance via the hypersecretion CAF-derived exosomes. Moving forward, therapies designed to interrupt the function of mecCAFs could be utilized to overcome matrix-mediated chemoresistance in PDAC. Citation Format: Weikun Xiao, Chae-Young Eun, Weian Zhao, Reginald Hill. Identification of mechanosensitive cancer associated fibroblasts in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5848.
Abstract 3464: Dynamics of resident memory (Trm) cell responses between skin and draining lymph nodes during primary and recall responses to melanoma
Authors: Cameron Messier, Nikhil Khatwani, Aaron Hawkes, Yuyang (Poppy) Huang, Mary Jo Turk
Journal: Cancer Research (2023)

Abstract Tissue resident memory (TRM) cells reside durably in tissues where they serve as a vital component of protective anti-tumor immunity. In mice, TRM cells are defined by their expression of tissue retention markers such as CD69 and CD103, and lack of egress markers such as CD62L, CCR7 and S1PR1. We previously showed that depletion of regulatory T cells induces the generation of protective CD8 Trm cells in skin and draining LNs of B16 melanoma tumor-excised mice. While tumor specific Trm cells were shown to stably reside in tissues at steady state, little is known about their migration between tissue compartments and circulation during primary and recall responses to melanoma. Using gp100-specific transgenic pmel CD8 T cells expressing a Kaede-GFP photoconvertible marker, we investigated the trafficking patterns of tumor Ag specific CD8+ T-cells that were labeled in situ by exposure to UV light in the skin. During primary tumor growth, we observed pronounced movement of antigen-experienced pmel cells through skin to tumor-draining LNs. This trafficking behavior could be inhibited by treatment with FTY720, indicating its S1PR-dependence. Such movement was no longer evident at memory timepoints. However, re-challenge with B16 cells in the dermis induced rapid pmel T cell egress to both LNs and circulation. Recallenge-mediated Trm cell skin egress was confirmed using anti-Thy1.1 monoclonal antibody to deplete circulating and lymphoid memory, while preserving skin TRM. Here we found that skin TRM proliferate and transiently increase expression of Tbet, but go on to generate a durable secondary Trm response in lymph nodes. These data highlight T cell movement between tissues during Trm programming and recall responses to cancer, and shed light on a potential mechanism for the generation TRM populations in tumor-draining lymph nodes. Moreover, our results highlight the potential for retrograde movement of Trm responses from peripheral tissue reservoirs to participate more broadly in systemic anti-tumor immunity. Citation Format: Cameron Messier, Nikhil Khatwani, Aaron Hawkes, Yuyang (Poppy) Huang, Mary Jo Turk. Dynamics of resident memory (Trm) cell responses between skin and draining lymph nodes during primary and recall responses to melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3464.
Abstract 501: Discovery of BPI-460372, a potent and selective inhibitor of TEAD for the treatment of solid tumors harboring Hippo pathway aberrations
Authors: Hongling Shen, Xiaofeng Xu, Hongfei Rong, Xizhen Song, Jinheng Gao, Jie Chen, Di Zhu, Xiangdong Zhao, Jun Tong, Zhengyao Zou, Xiaoyun Liu, Jin Guo, Yan Xu, Yabin Li, Xiangyong Liu, Hong Chen, Jiayu Zhao, Yanju Liu, Xuepeng Ju, Haibo Chen, Hong Lan, Lieming Ding, Jiabing Wang
Journal: Cancer Research (2023)

Abstract The Hippo signaling pathway is critical for the regulation of organ development, tissue homeostasis, and tumorigenesis by controlling the activation status of yes-associated protein (YAP) or its homolog PDZ-binding motif (TAZ). As a major downstream effector, the transcription factor TEAD is activated by forming a complex with YAP/TAZ. Hippo pathway aberrations, such as NF2-deficiency or LATS1/2 mutations leading to hyperactivation of YAP/TAZ and subsequent activation of TEAD, have been reported in many cancers, including mesothelioma, meningioma, soft tissue sarcoma and non-small cell lung cancer. Inhibiting TEAD auto-palmitoylation by directly blocking the palmitoylation pocket of TEAD is a potential therapeutic approach for cancer treatment. Here we present BPI-460372, a novel small molecule that directly blocks the TEAD auto-palmitoylation. BPI-460372 covalently and irreversibly binds to the cysteine residue in the TEAD palmitoylation pocket, preventing TEAD palmitoylation and inhibiting its biological function. BPI-460372 significantly inhibits the expression of a TEAD-responsive element reporter, as well as the mRNA of downstream target genes such as CTGF and CYR61 in NF2-deficient cells. At the cellular level, BPI-460372 strongly inhibited the proliferation of tumor cells harboring Hippo pathway aberrations. BPI-460372 also significantly suppressed tumor growth in NF2-deficient or LATS1/2 mutation xenograft models. In addition, BPI-460372 exhibited excellent oral bioavailability, high exposure across multiple species, and adequate ADME properties. In conclusion, BPI-460372 is a potent and selective TEAD palmitoylation inhibitor for the treatment of solid tumors harboring Hippo pathway aberrations. It is planned to enter Phase I clinical trial in China in early 2023. Citation Format: Hongling Shen, Xiaofeng Xu, Hongfei Rong, Xizhen Song, Jinheng Gao, Jie Chen, Di Zhu, Xiangdong Zhao, Jun Tong, Zhengyao Zou, Xiaoyun Liu, Jin Guo, Yan Xu, Yabin Li, Xiangyong Liu, Hong Chen, Jiayu Zhao, Yanju Liu, Xuepeng Ju, Haibo Chen, Hong Lan, Lieming Ding, Jiabing Wang. Discovery of BPI-460372, a potent and selective inhibitor of TEAD for the treatment of solid tumors harboring Hippo pathway aberrations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 501.
Abstract 3955: Functional evaluation of pancreatic cancer prognostic marker, LXN, utilizing multiomics analysis based on patient-derived cancer model
Authors: Chan Hee Park, Hee Seung Lee, Jin Su Kim, Yoo Keung Tae, Jin Young Lee, Seungmin Bang
Journal: Cancer Research (2023)

Abstract Background: Pancreatic cancer is the most dreadful malignant tumor and expected becoming the second cause of death in 2030. Despites of vigorous studies, there were no definitive prognostic biomoleculars marker for pancreatic cancer. Herein, we already established primary pancreatic cancer cell lines from the real patients of pancreatic cancer, using conditionally reprogrammed cell culture (CRC). We tried to find novel prognostic biomarkers with multi-omics analysis of our primary pancreatic cancer cell lines. Methods: In this study, we selected pancreatic cancer prognostic markers using established CRCs and FFPE samples and validated the molecular mechanism of LXN. As the first step, we performed both transcriptome and proteome analysis using RNA sequencing and liquid chromatography-tandem mass spectrometry (LC/MS-MS) with 6 primary pancreatic cancer cell lines established by CRC. After analysis, we mined several candidate markers of prognosis including latexin (LXN) and sialic acid acetylesterease (SIAE). And we validated these markers clinicopathologically using immunohistochemical (IHC) staining of 136 tissues from a different set of pancreatic cancer patients. And we confirmed the knock-down effect of LXN using siLXN in pancreatic cancer cells. Results: We selected 2 highly prognostic markers with LXN and SIAE after transcriptome and proteome analysis. In these genes, high LXN expression group showed longer median overall survival (OS) than low expression group, respectively (14.8 vs. 10.4 months, P-value=0.28), respectively. For the evaluation of IHC, we established 3D organoid model using CRCs and confirmed the correlation between mRNA expression and protein expression with western blotting and IHC. The expression of Akt/mTOR was decreased after siLXN treatment compared to control groups. In order to validation as a prognostic marker, we stained formalin-fixed, paraffin-embedded (FFPE) slide from 136 pancreatic cancer patients. After IHC analysis, LXN high group (H-score &amp;gt; 12) showed significantly longer OS than low LXN group (52 vs. 28 months, P-value = 0.043). Conclusion: In this study, we found LXN as a prognostic marker with inhibition of proliferation utilizing patient-derived cancer model and FFPE samples. Citation Format: Chan Hee Park, Hee Seung Lee, Jin Su Kim, Yoo Keung Tae, Jin Young Lee, Seungmin Bang. Functional evaluation of pancreatic cancer prognostic marker, LXN, utilizing multiomics analysis based on patient-derived cancer model. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3955.
Abstract 3595: Epigenetic driven IL32 expression contributes to a JNK related cell stress response in breast cancer stem cells to promote cellular invasion
Authors: Megan A. Wilson, Elayne M. Benson, Emma Gray, Paige Cairns, Maria Ouzounova, Hasan Korkaya, Austin Y. Shull
Journal: Cancer Research (2023)

Abstract Metastatic potential in basal-like breast cancers typically correspond with increased enrichment of EpCAM-/CD49f- cancer stem cells (CSC). With this premise in mind, it is important to better understand the mechanistic driver of these cell populations and their distinctive potential to interact with the tumor microenvironment (TME) for cancer promotion. Previous work from our lab has compared the 450K DNA methylation profile of EpCAM-/CD49f- poor breast cancer cell lines to that of EpCAM-/CD49f- enriched breast cancer cell lines and found the IL32 promoter to be hypomethylated in EpCAM-/CD49f- enriched cell lines, a result which corresponded basal-like patient samples in TCGA. By identifying IL32 being differentially regulated in CSC-enriched cell lines, we further sought to characterize IL32’s role in breast cancer aggressiveness. We first were able to identify several overarching mechanisms altered in siIL32 treated SUM15PT cells by RNAseq differential expression analysis (FDR p-value &amp;lt;0.01). Most notable from our RNAseq results was the significant enrichment of upregulated pathways involved in extracellular matrix (ECM) organization as well as significant enrichment of downregulated pathways involved in cellular and replicative stress responses. Particular examples of transcripts differentially expressed between control and siIL32-treated SUM159PT cells included COL6A1, ITGB3, and CD24 that were upregulated as well as NQO1, HMOX1, and CXCL2/CXCL3 that were downregulated. Furthermore, IL32 suppression decreased SUM159PT invasion in both an ECM-matrix cell invasion assay and a chick CAM xenograft/angiogenesis model. From our RNAseq results, we then performed a multi-pathway protein phosphorylation array to determine whether any key signaling events were affected by siIL32 knockdown in SUM159PT cells. Based on this approach, we were able observe a significant decrease in phosphorylated JNK and phosphorylated NFKB in siL32-treated cells when compared to control, both of which are well-established events that can coordinate both cell stress responses and cellular invasion. Collectively, our results reflect the notion that differential IL32 expression by promoter hypomethylation in breast CSCs plays a role to mitigating intracellular stress and subsequently allowing for breast cancer cell invasion and metastasis. Citation Format: Megan A. Wilson, Elayne M. Benson, Emma Gray, Paige Cairns, Maria Ouzounova, Hasan Korkaya, Austin Y. Shull. Epigenetic driven IL32 expression contributes to a JNK related cell stress response in breast cancer stem cells to promote cellular invasion. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3595.
Abstract 4750: TWIST2 mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma
Authors: Akansha M. Shah, Lei Guo, Maria Gabriella Morales, Priscilla Jaichander, Kenian Chen, Huocong Huang, Karla Cano Hernandez, Lin Xu, Rhonda Bassel-Duby, Eric N. Olson, Ning Liu
Journal: Cancer Research (2023)

Abstract Rhabdomyosarcoma (RMS) is a common soft tissue sarcoma in children that resembles the developing skeletal muscle. Unlike normal muscle cells, RMS cells fail to differentiate despite expression of the myogenic determination protein MYOD. The TWIST2 transcription factor is frequently overexpressed in fusion-negative RMS (FN-RMS). TWIST2 blocks differentiation by inhibiting MYOD activity in myoblasts, but its role in FN-RMS pathogenesis is incompletely understood. Here, we show that knockdown of TWIST2 enables FN-RMS cells to exit the cell cycle and undergo terminal myogenesis. TWIST2 knockdown also substantially reduces tumor growth in a xenograft model of FN-RMS. Mechanistically, TWIST2 controls H3K27 acetylation at distal enhancers by interacting with the chromatin remodelers SMARCA4 and CHD3 to activate growth-related and repress myogenesis-related target genes, respectively. These findings provide novel insights into the role of TWIST2 in maintaining an undifferentiated and tumorigenic state of FN-RMS and highlight the potential of suppressing TWIST2-regulated pathways to treat FN-RMS. Citation Format: Akansha M. Shah, Lei Guo, Maria Gabriella Morales, Priscilla Jaichander, Kenian Chen, Huocong Huang, Karla Cano Hernandez, Lin Xu, Rhonda Bassel-Duby, Eric N. Olson, Ning Liu. TWIST2 mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4750.